[1][2][3] Before the arrival of the Spanish in the 16th century, the present-day city of Isabela was initially a Yakan community called Pasengen, and Pagpasalan.

In 1881, the mission chapel of the Jesuits located between the Fort Isabela II and the shore saw growth in number of Christian adherents.

It was dedicated to Saint Elizabeth of Portugal, in relation to the naming of the nearby fort in honor of Queen Isabella II of Spain.

[3] The earthquake of September 21, 1897 and its resulting destructions prompted to relocate the church site to its present location in Barangay Seaside.

[1][3] Bishop José María Querejeta Mendizábal, C.M.F., the prelature's first bishop-prelate,[1] was installed on February 15, 1964[3] and in the same year, he spearheaded the construction of the present cathedral.